Hiroshi Sugiyama Department of Chemistry, Graduate School of Science Institute for Integrated Cell-Material Sciences (iCeMS)

Kyoto University1

100 nm

生体分子機能論 2018-6水素引き抜き抗生物質

Advanced Course in Molecular Biology and Biochemistry

Basics1 Basic elements of nucleic acids and their synthesis

2 Sequencing of DNA

3 3D structure of DNA 1

4 3D structure of DNA 2

Chemistry 5) DNA alkylation

6) Hydrogen abstraction 1

7) Hydrogen abstraction 2

8) Charge transfer

Biology 9) Epigenetics 1

10) Epigenetics 2

11) ATRX

Hydrogen (H) atom abstraction:

H atom is abstracted from a substrate according to the general

reaction

X H-Y X-H+ Y+. .

Fe(V)-oxo Cytochrome p450

Tet protein

Carbon radical Calicheamicin g1

C-1027, Dynemicin A, Esperamicin A1

RH + O2 + NADPH + H+ → ROH + H2O +

NADP+

Bleomycin

Bergman cyclization

s radial not p radical

Antitumor antibiotics which induce DNA strand scission by H abstraction

Gemtuzumab ozogamicin:

(Mylotarg)

Calicheamycin analog CD33

monoclonal antibody

Conjugate

(acute myeloid leukemia)

used from 2000-2010

Increased patient death and no

benefit over conventional cancer

therapy

Formation of carbon racial from Calicheamycin and Neocarzinostatin

4’ OH

4’ O2

H abstraction from deoxyribose backbone

Science 1989, 245, 1396

Specific Detection of C-4’Hydroxylated

Abasic Sites Generated by Bleomycin and

Neocarzinostatin in DNA

Hiroshi Sugiyama, Hiroshi Kawabata, Tsuyoshi Fujiwara,

Yukihiro Dannoue, and Isao Saito*

Contribution from the Department of Synthetic Chemistry,

Faculty of Engineering, Kyoto University, Kyoto 606, Japan.

Received November 27, 1989

J. Am.Chem. Soc.1990,112,5252-5257

Enzymatic Digestion of Oligonucleotides Containing

3’-Pyridazinylmethyl Termini

Detection of Pyridazine Mononucleotide

from Co-PEM-Treated DNA

Co-PEM induces C-4‘ hydroxylation preferentially at GC and GT sites

and also mediates the release of A and T from poly(dT-dA).

Fe-PEM induces strand cleavage with the formation of glycolic acid termini at the 3’-end

C-4’ hydroxylation is estimated to be a minimum of 17% of the total event (5.0μM/29.2μM)

PDBID:2R2S

PDBID:1GJ2

Co(III) bleomycin : stable but it cleaves DNA under UV irradiation condition

Biochemistry (2001) 40, 5894-5905

Crystal structure of DNA-bound Co(III)bleomycin B2:

Insights on intercalation and minor groove bindingProc Natl Acad Sci USA,2008,105:5052-5056

Bithiazole(BT) Intercalation

DNAs superinposed

in the Presence and Absence of Co-BLM

20

DNMT TET

5-hydorxymethylcytosine(hmC)

5-formylcytosine(fC)

5-carboxylcytosine(caC)

TET TET

TDG and BER

cytosine(C)

5-methylcytosine(mC)

decarboxylase?

Demethylation by TET protein

• DNA repair protein, TDG (thymine DNA glycosylase) , has the activity to excise fC and caC

• Decarboxylation of caC to form C may occur, although the decarboxylase has not been discovered yet

21

Oxidation by TET preferentially occurs at linker DNA

Investigating Nucleosome Accessibility for MNase, FeII  Peplomycin, and

Duocarmycin B2 by Using Capillary Electrophoresis

Zou, T.; Kizaki, S.; Sugiyama, H.

ChemBioChem. 2018, 19, 664-668.

Metallo-Bleomycin Cleaves Parallel-Stranded DNA

Similarly to B-DNA. Ikeda, S.; Saito, I.; Sugiyama, H.

Tetrahedron Lett., 2000, 41, 3919-3922.